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Detailed information for vg0135984669:

Variant ID: vg0135984669 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35984669
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAGACGTAGATGATCCTCGGCAGCCGGTGCTTGTCCGGCCTCCACAGCTCTCCCTTGAGAACCTGCCACCTCTCCTTCAGCTTGGCCAGAGCACCCTG[C/G]
ACCACCATGATCGTCGCGGCGTGCCGCTTGTTGAAGTCGGCTTTCGCCGGAGATAGATCCTTCTCACGGTATGGAGTCATCAGCCAGGGAAGGAGAGGGT

Reverse complement sequence

ACCCTCTCCTTCCCTGGCTGATGACTCCATACCGTGAGAAGGATCTATCTCCGGCGAAAGCCGACTTCAACAAGCGGCACGCCGCGACGATCATGGTGGT[G/C]
CAGGGTGCTCTGGCCAAGCTGAAGGAGAGGTGGCAGGTTCTCAAGGGAGAGCTGTGGAGGCCGGACAAGCACCGGCTGCCGAGGATCATCTACGTCTGCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.40% 47.40% 0.11% 0.08% NA
All Indica  2759 26.60% 73.20% 0.11% 0.14% NA
All Japonica  1512 98.20% 1.80% 0.00% 0.00% NA
Aus  269 41.60% 58.40% 0.00% 0.00% NA
Indica I  595 11.10% 88.60% 0.00% 0.34% NA
Indica II  465 6.20% 93.80% 0.00% 0.00% NA
Indica III  913 40.60% 59.30% 0.11% 0.00% NA
Indica Intermediate  786 34.00% 65.50% 0.25% 0.25% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 7.30% 1.04% 0.00% NA
Intermediate  90 65.60% 33.30% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135984669 C -> G LOC_Os01g62160.1 synonymous_variant ; p.Val303Val; LOW synonymous_codon Average:83.606; most accessible tissue: Zhenshan97 flower, score: 92.407 N N N N
vg0135984669 C -> DEL LOC_Os01g62160.1 N frameshift_variant Average:83.606; most accessible tissue: Zhenshan97 flower, score: 92.407 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0135984669 C G -0.01 -0.01 0.0 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135984669 NA 2.70E-08 mr1068 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 8.22E-11 mr1078 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 1.32E-07 mr1096 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 3.84E-06 mr1121 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 8.56E-09 mr1133 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 4.55E-09 mr1887 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 1.58E-08 mr1078_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 9.86E-08 mr1133_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0135984669 NA 1.11E-06 mr1870_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251